基于基因组区间的功能富集分析。
基本信息
| 软件包 | 链接 |
|---|---|
| 编程语言 | R, C++ |
| Bioconductor | https://bioconductor.org/packages/rGREAT/ |
| GitHub | https://github.com/jokergoo/rGREAT |
| 文档 | https://jokergoo.github.io/rGREAT/ |
| 论文 | Zuguang Gu, et al., rGREAT: an R/bioconductor package for functional enrichment on genomic regions. Bioinformatics 2023. |
例子
library(rGREAT)
gr = randomRegions(nr = 1000, genome = "hg19")
res = great(gr, "MSigDB:H", "TxDb.Hsapiens.UCSC.hg19.knownGene")
tb = getEnrichmentTable(res)
head(tb)
## id genome_fraction observed_region_hits
## 1 HALLMARK_GLYCOLYSIS 0.01939528 33
## 2 HALLMARK_HYPOXIA 0.02259297 31
## 3 HALLMARK_KRAS_SIGNALING_UP 0.02807810 35
## 4 HALLMARK_BILE_ACID_METABOLISM 0.01007710 15
## 5 HALLMARK_IL6_JAK_STAT3_SIGNALING 0.00588037 9
## 6 HALLMARK_ESTROGEN_RESPONSE_LATE 0.01976179 24
## fold_enrichment p_value p_adjust mean_tss_dist observed_gene_hits
## 1 1.849397 0.0007344439 0.03231553 183608 30
## 2 1.491422 0.0201847210 0.44406386 258881 26
## 3 1.354917 0.0467663453 0.55023294 262881 30
## 4 1.617960 0.0500211761 0.55023294 133541 13
## 5 1.663604 0.0975349984 0.74772933 134220 9
## 6 1.320070 0.1070182007 0.74772933 214394 20
## gene_set_size fold_enrichment_hyper p_value_hyper p_adjust_hyper
## 1 199 2.016169 0.0001799407 0.00263913
## 2 199 1.747346 0.0038037314 0.04184105
## 3 197 2.036637 0.0001499209 0.00263913
## 4 112 1.552330 0.0748775119 0.34746615
## 5 81 1.485991 0.1501078147 0.47176742
## 6 198 1.350901 0.1043818323 0.35329236